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1JD2
Asym. Unit
Info
Asym.Unit (1.0 MB)
Biol.Unit 1, α-C (1.0 MB)
Biol.Unit 1 (1.0 MB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE YEAST 20S PROTEASOME:TMC-95A COMPLEX: A NON-COVALENT PROTEASOME INHIBITOR
Authors
:
M. Groll, Y. Koguchi, R. Huber, J. Kohno
Date
:
12 Jun 01 (Deposition) - 13 Feb 02 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.00
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,1,2,8,9
Biol. Unit 1: A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,1,2,8,9 (1x)
Keywords
:
Beta-Sandwich, Proteasome:Inhibitor Complex, Hydrolase, Hydrolase- Hydrolase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Groll, Y. Koguchi, R. Huber, J. Kohno
Crystal Structure Of The 20 S Proteasome:Tmc-95A Complex: A Non-Covalent Proteasome Inhibitor.
J. Mol. Biol. V. 311 543 2001
[
close entry info
]
Hetero Components
(4, 16)
Info
All Hetero Components
1a: (3S)-3-METHYL-2-OXOPENTANOIC ACID (1QQa)
1b: (3S)-3-METHYL-2-OXOPENTANOIC ACID (1QQb)
2a: (1Z)-PROP-1-EN-1-AMINE (AKKa)
2b: (1Z)-PROP-1-EN-1-AMINE (AKKb)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
3e: MAGNESIUM ION (MGe)
3f: MAGNESIUM ION (MGf)
3g: MAGNESIUM ION (MGg)
3h: MAGNESIUM ION (MGh)
3i: MAGNESIUM ION (MGi)
3j: MAGNESIUM ION (MGj)
4a: (2S,3R)-2-AZANYL-3-HYDROXY-3-[(3S)... (R4Ka)
4b: (2S,3R)-2-AZANYL-3-HYDROXY-3-[(3S)... (R4Kb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
1QQ
2
Mod. Amino Acid
(3S)-3-METHYL-2-OXOPENTANOIC ACID
2
AKK
2
Mod. Amino Acid
(1Z)-PROP-1-EN-1-AMINE
3
MG
10
Ligand/Ion
MAGNESIUM ION
4
R4K
2
Mod. Amino Acid
(2S,3R)-2-AZANYL-3-HYDROXY-3-[(3S)-3-HYDROXY-2-OXO-1H-INDOL-3-YL]PROPANOIC ACID
[
close Hetero Component info
]
Sites
(11, 11)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
THR G:13 , TYR G:123 , ARG G:126 , MET G:129 , HOH G:248
BINDING SITE FOR RESIDUE MG G 1
02
AC2
SOFTWARE
GLU D:105 , HOH D:253 , TYR L:66 , SER L:75 , SER L:78 , HOH L:206 , HOH L:211
BINDING SITE FOR RESIDUE MG D 2
03
AC3
SOFTWARE
TYR A:8 , SER F:13 , ASN F:127 , HOH F:244 , ALA G:127 , HOH G:672
BINDING SITE FOR RESIDUE MG F 243
04
AC4
SOFTWARE
ILE H:163 , ASP H:166 , LEU H:167 , SER H:169 , HOH H:2265 , ASP S:194
BINDING SITE FOR RESIDUE MG H 224
05
AC5
SOFTWARE
HOH H:812 , SER I:131 , HOH I:216 , HOH I:771
BINDING SITE FOR RESIDUE MG I 195
06
AC6
SOFTWARE
ALA I:163 , ASP I:166 , SER I:169 , HOH I:205 , HOH I:209
BINDING SITE FOR RESIDUE MG I 196
07
AC7
SOFTWARE
THR L:163 , HIS L:166 , VAL L:169 , HOH L:254 , HOH L:2847
BINDING SITE FOR RESIDUE MG L 195
08
AC8
SOFTWARE
ILE N:163 , ASP N:166 , SER N:169 , HOH N:554
BINDING SITE FOR RESIDUE MG N 188
09
AC9
SOFTWARE
ARG K:19 , ALA K:163 , ASP K:166 , ALA K:167 , SER K:169 , HOH K:2446 , ASP P:194
BINDING SITE FOR RESIDUE MG P 195
10
BC1
SOFTWARE
HOH 8:250 , HOH 8:652 , THR H:1 , SER H:20 , THR H:21 , GLN H:22 , GLY H:23 , ALA H:27 , LYS H:33 , GLY H:47 , ALA H:49 , HOH H:795 , SER I:-5 , ASP I:114 , LEU I:115
BINDING SITE FOR CHAIN 8 OF TMC-95A INHIBITOR
11
BC2
SOFTWARE
HOH 9:2652 , THR O:1 , SER O:20 , THR O:21 , GLN O:22 , GLY O:23 , ALA O:27 , LYS O:33 , GLY O:47 , ALA O:49 , HOH O:2250 , SER P:-5 , ASP P:114 , LEU P:115 , HOH P:1346
BINDING SITE FOR CHAIN 9 OF TMC-95A INHIBITOR
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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]
PROSITE Patterns/Profiles
(4, 48)
Info
All PROSITE Patterns/Profiles
1: PROTEASOME_BETA_2 (J:-1-178,Q:-1-178,I:-1-178,P:-1-17...)
2: PROTEASOME_ALPHA_1 (C:8-30,X:8-30,A:8-30,V:8-30,E:8-30...)
3: PROTEASOME_BETA_1 (J:4-51,Q:4-51,I:4-51,P:4-51,N:4-51...)
4: PROTEASOME_ALPHA_2 (C:23-233,X:23-233,A:23-233,V:23-23...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PROTEASOME_BETA_2
PS51476
Proteasome beta-type subunit profile.
PSB4_YEAST
1-184
2
J:-1-178
Q:-1-178
PSB3_YEAST
9-190
2
I:-1-178
P:-1-178
PSB6_YEAST
28-226
2
L:-1-178
S:-1-178
PSB7_YEAST
41-233
2
M:-1-178
T:-1-178
2
PROTEASOME_ALPHA_1
PS00388
Proteasome alpha-type subunits signature.
PSA4_YEAST
4-26
2
C:8-30
X:8-30
PSA2_YEAST
5-27
2
A:8-30
V:8-30
PSA6_YEAST
6-28
2
E:8-30
Z:8-30
PSA3_YEAST
6-28
2
B:8-30
W:8-30
PSA7_YEAST
8-30
2
1:8-30
F:8-30
PSA1_YEAST
12-34
2
2:8-30
G:8-30
3
PROTEASOME_BETA_1
PS00854
Proteasome beta-type subunits signature.
PSB4_YEAST
5-52
2
J:4-51
Q:4-51
PSB3_YEAST
13-59
2
I:4-51
P:4-51
PSB1_YEAST
23-70
2
N:4-51
U:4-51
PSB6_YEAST
32-79
2
L:4-51
S:4-51
PSB2_YEAST
33-80
2
H:4-51
O:4-51
PSB7_YEAST
45-92
2
M:4-51
T:4-51
PSB5_YEAST
79-126
2
K:4-51
R:4-51
4
PROTEASOME_ALPHA_2
PS51475
Proteasome alpha-type subunit profile.
PSA4_YEAST
19-233
2
C:23-233
X:23-233
PSA2_YEAST
20-247
2
A:23-233
V:23-233
PSA6_YEAST
21-234
2
E:23-233
Z:23-233
PSA3_YEAST
21-239
2
B:23-233
W:23-233
PSA5_YEAST
23-240
2
D:23-233
Y:23-233
PSA7_YEAST
23-240
2
1:23-233
F:23-233
PSA1_YEAST
27-245
2
2:23-233
G:23-233
[
close PROSITE info
]
Exons
(15, 30)
Info
All Exons
Exon 1.1 (L:-9-194 (gaps) | S:-9-194 (gaps))
Exon 2.1 (J:-1-193 (gaps) | Q:-1-193 (gaps))
Exon 3.1 (I:-8-194 (gaps) | P:-8-194 (gaps))
Exon 4.1 (M:-8-211 (gaps) | T:-8-211 (gaps))
Exon 5.1 (2:6-240 (gaps) | G:6-240 (gaps))
Exon 6.1 (B:4-239 (gaps) | W:4-239 (gaps))
Exon 7.1 (D:9-244 (gaps) | Y:9-244 (gaps))
Exon 8.1 (N:1-3 | U:1-3)
Exon 8.2 (N:3-187J (gaps) | U:3-187J (gaps))
Exon 9.1 (A:4-236 (gaps) | V:4-236 (gaps))
Exon 10.1 (E:4-233 (gaps) | Z:4-233 (gaps))
Exon 11.1 (C:7-243 (gaps) | X:7-243 (gaps))
Exon 12.1 (H:1-223 (gaps) | O:1-223 (gaps))
Exon 13.1 (1:5-241 (gaps) | F:5-241 (gaps))
Exon 14.1 (K:1-211 (gaps) | R:1-211 (gaps))
View:
Select:
Label:
All Exon Boundaries
01: Boundary -/1.1
02: Boundary 1.1/-
03: Boundary -/2.1
04: Boundary 2.1/-
05: Boundary -/3.1
06: Boundary 3.1/-
07: Boundary -/4.1
08: Boundary 4.1/-
09: Boundary -/5.1
10: Boundary 5.1/-
11: Boundary -/6.1
12: Boundary 6.1/-
13: Boundary -/7.1
14: Boundary 7.1/-
15: Boundary -/8.1
16: Boundary 8.1/8.2
17: Boundary 8.2/-
18: Boundary -/9.1
19: Boundary 9.1/-
20: Boundary -/10.1
21: Boundary 10.1/-
22: Boundary -/11.1
23: Boundary 11.1/-
24: Boundary -/12.1
25: Boundary 12.1/-
26: Boundary -/13.1
27: Boundary 13.1/-
28: Boundary -/14.1
29: Boundary 14.1/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1
YBL041W
1
YBL041W.1
II:141250-141975
726
PSB6_YEAST
1-241
241
2
L:-9-194 (gaps)
S:-9-194 (gaps)
223
223
2.1
YER012W
1
YER012W.1
V:177834-178430
597
PSB4_YEAST
1-198
198
2
J:-1-193 (gaps)
Q:-1-193 (gaps)
199
199
3.1
YER094C
1
YER094C.1
V:349342-348725
618
PSB3_YEAST
1-205
205
2
I:-8-194 (gaps)
P:-8-194 (gaps)
206
206
4.1
YFR050C
1
YFR050C.1
VI:249853-249053
801
PSB7_YEAST
1-266
266
2
M:-8-211 (gaps)
T:-8-211 (gaps)
238
238
5.1
YGL011C
1
YGL011C.1
VII:475252-474494
759
PSA1_YEAST
1-252
252
2
2:6-240 (gaps)
G:6-240 (gaps)
248
248
6.1
YGR135W
1
YGR135W.1
VII:761397-762173
777
PSA3_YEAST
1-258
258
2
B:4-239 (gaps)
W:4-239 (gaps)
245
245
7.1
YGR253C
1
YGR253C.1
VII:999145-998363
783
PSA5_YEAST
1-260
260
2
D:9-244 (gaps)
Y:9-244 (gaps)
249
249
8.1
YJL001W
1
YJL001W.1
X:435156-435220
65
PSB1_YEAST
1-22
22
2
N:1-3
U:1-3
3
3
8.2
YJL001W
2
YJL001W.2
X:435337-435919
583
PSB1_YEAST
22-215
194
2
N:3-187J (gaps)
U:3-187J (gaps)
197
197
9.1
YML092C
1
YML092C.1
XIII:86739-85987
753
PSA2_YEAST
1-250
250
2
A:4-236 (gaps)
V:4-236 (gaps)
251
251
10.1
YMR314W
1
YMR314W.1
XIII:901708-902412
705
PSA6_YEAST
1-234
234
2
E:4-233 (gaps)
Z:4-233 (gaps)
240
240
11.1
YOL038W
1
YOL038W.1
XV:255336-256100
765
PSA4_YEAST
1-254
254
2
C:7-243 (gaps)
X:7-243 (gaps)
244
244
12.1
YOR157C
1
YOR157C.1
XV:631752-630967
786
PSB2_YEAST
1-261
261
2
H:1-223 (gaps)
O:1-223 (gaps)
224
224
13.1
YOR362C
1
YOR362C.1
XV:1018744-1017878
867
PSA7_YEAST
1-288
288
2
1:5-241 (gaps)
F:5-241 (gaps)
248
248
14.1
YPR103W
1
YPR103W.1
XVI:732347-733210
864
PSB5_YEAST
1-287
287
2
K:1-211 (gaps)
R:1-211 (gaps)
213
213
[
close EXON info
]
SCOP Domains
(2, 28)
Info
All SCOP Domains
1a: SCOP_d1jd2a_ (A:)
1b: SCOP_d1jd2b_ (B:)
1c: SCOP_d1jd2c_ (C:)
1d: SCOP_d1jd2d_ (D:)
1e: SCOP_d1jd2e_ (E:)
1f: SCOP_d1jd2f_ (F:)
1g: SCOP_d1jd2g_ (G:)
1h: SCOP_d1jd2o_ (O:)
1i: SCOP_d1jd2p_ (P:)
1j: SCOP_d1jd2q_ (Q:)
1k: SCOP_d1jd2r_ (R:)
1l: SCOP_d1jd2s_ (S:)
1m: SCOP_d1jd2t_ (T:)
1n: SCOP_d1jd2u_ (U:)
2a: SCOP_d1jd21_ (1:)
2b: SCOP_d1jd22_ (2:)
2c: SCOP_d1jd2h_ (H:)
2d: SCOP_d1jd2i_ (I:)
2e: SCOP_d1jd2j_ (J:)
2f: SCOP_d1jd2k_ (K:)
2g: SCOP_d1jd2l_ (L:)
2h: SCOP_d1jd2m_ (M:)
2i: SCOP_d1jd2n_ (N:)
2j: SCOP_d1jd2v_ (V:)
2k: SCOP_d1jd2w_ (W:)
2l: SCOP_d1jd2x_ (X:)
2m: SCOP_d1jd2y_ (Y:)
2n: SCOP_d1jd2z_ (Z:)
View:
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Classes
(
)
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)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Ntn hydrolase-like
(356)
Superfamily
:
N-terminal nucleophile aminohydrolases (Ntn hydrolases)
(352)
Family
:
Proteasome subunits
(222)
Protein domain
:
Proteasome alpha subunit (non-catalytic)
(66)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(54)
1a
d1jd2a_
A:
1b
d1jd2b_
B:
1c
d1jd2c_
C:
1d
d1jd2d_
D:
1e
d1jd2e_
E:
1f
d1jd2f_
F:
1g
d1jd2g_
G:
1h
d1jd2o_
O:
1i
d1jd2p_
P:
1j
d1jd2q_
Q:
1k
d1jd2r_
R:
1l
d1jd2s_
S:
1m
d1jd2t_
T:
1n
d1jd2u_
U:
Protein domain
:
Proteasome beta subunit (catalytic)
(61)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(51)
2a
d1jd21_
1:
2b
d1jd22_
2:
2c
d1jd2h_
H:
2d
d1jd2i_
I:
2e
d1jd2j_
J:
2f
d1jd2k_
K:
2g
d1jd2l_
L:
2h
d1jd2m_
M:
2i
d1jd2n_
N:
2j
d1jd2v_
V:
2k
d1jd2w_
W:
2l
d1jd2x_
X:
2m
d1jd2y_
Y:
2n
d1jd2z_
Z:
[
close SCOP info
]
CATH Domains
(1, 28)
Info
all CATH domains
1a: CATH_1jd2L00 (L:-9-194)
1b: CATH_1jd2E00 (E:4-233)
1c: CATH_1jd2Z00 (Z:4-233)
1d: CATH_1jd2K00 (K:1-211)
1e: CATH_1jd2R00 (R:1-211)
1f: CATH_1jd2C00 (C:7-243)
1g: CATH_1jd2X00 (X:7-243)
1h: CATH_1jd2200 (2:6-240)
1i: CATH_1jd2G00 (G:6-240)
1j: CATH_1jd2S00 (S:-9-194)
1k: CATH_1jd2B00 (B:4-239)
1l: CATH_1jd2W00 (W:4-239)
1m: CATH_1jd2100 (1:5-241)
1n: CATH_1jd2F00 (F:5-241)
1o: CATH_1jd2N00 (N:1-187J)
1p: CATH_1jd2U00 (U:1-187J)
1q: CATH_1jd2I00 (I:-8-194)
1r: CATH_1jd2P00 (P:-8-194)
1s: CATH_1jd2A00 (A:4-236)
1t: CATH_1jd2V00 (V:4-236)
1u: CATH_1jd2J00 (J:-1-193)
1v: CATH_1jd2Q00 (Q:-1-193)
1w: CATH_1jd2H00 (H:1-223)
1x: CATH_1jd2O00 (O:1-223)
1y: CATH_1jd2D00 (D:9-244)
1z: CATH_1jd2Y00 (Y:9-244)
1aa: CATH_1jd2M00 (M:-8-211)
1ab: CATH_1jd2T00 (T:-8-211)
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Classes
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(
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Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
4-Layer Sandwich
(459)
Topology
:
Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
(128)
Homologous Superfamily
:
Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
(124)
Baker's yeast (Saccharomyces cerevisiae)
(14)
1a
1jd2L00
L:-9-194
1b
1jd2E00
E:4-233
1c
1jd2Z00
Z:4-233
1d
1jd2K00
K:1-211
1e
1jd2R00
R:1-211
1f
1jd2C00
C:7-243
1g
1jd2X00
X:7-243
1h
1jd2200
2:6-240
1i
1jd2G00
G:6-240
1j
1jd2S00
S:-9-194
1k
1jd2B00
B:4-239
1l
1jd2W00
W:4-239
1m
1jd2100
1:5-241
1n
1jd2F00
F:5-241
1o
1jd2N00
N:1-187J
1p
1jd2U00
U:1-187J
1q
1jd2I00
I:-8-194
1r
1jd2P00
P:-8-194
1s
1jd2A00
A:4-236
1t
1jd2V00
V:4-236
1u
1jd2J00
J:-1-193
1v
1jd2Q00
Q:-1-193
1w
1jd2H00
H:1-223
1x
1jd2O00
O:1-223
1y
1jd2D00
D:9-244
1z
1jd2Y00
Y:9-244
1aa
1jd2M00
M:-8-211
1ab
1jd2T00
T:-8-211
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Chain D
Chain E
Chain F
Chain G
Chain H
Chain I
Chain J
Chain K
Chain L
Chain M
Chain N
Chain O
Chain P
Chain Q
Chain R
Chain S
Chain T
Chain U
Chain V
Chain W
Chain X
Chain Y
Chain Z
Chain 1
Chain 2
Chain 8
Chain 9
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
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RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (1.0 MB)
Header - Asym.Unit
Biol.Unit 1 (1.0 MB)
Header - Biol.Unit 1
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(also compressed with 'gzip', see the
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for a complete list)
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